Thanks, Jason! One more quick question. The data output file specified by
monitor_file. Does that correspond to the reweighed free energies or simply
the biasing energy added to each region of the reaction coordinate? i.e.
can I extract the free energy from this output file? I appreciate your help.
Geoffrey
On Mon, Apr 21, 2014 at 12:58 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, 2014-04-21 at 09:29 -0400, Geoffrey Gray wrote:
> > Hi, I am running ABMD simulations using the flooding mode. The
> > documentation says that these free energies can be accessed from the .nc
> > output using the ncsu-umbrella-slice utility. However, I cannot find this
> > program. How can I access the free energy profile? Thanks
>
> We've just put the ncsu-umbrella-slice source code under the "downloads"
> section of the Amber website.
>
> You'll have to configure and compile the code there. Something like
> this:
>
> cd ncsu-umbrella-slice/
> ./configure --with-netcdf-prefix=$AMBERHOME
> make
> make install
>
> This should install the program to /usr/local/bin (or you can specify
> --prefix to configure to have it install elsewhere).
>
> For the record, this code is quite old and is not really supported
> anymore (I don't know of any developers actively using the NCSU
> functionality). So you will probably get only very limited (if any)
> support from the mailing list.
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
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Received on Mon Apr 21 2014 - 11:00:02 PDT
